AMBER Archive (2009)

Subject: Re: [AMBER] Problem with MM-PBSA energy calculation

From: Barbault Florent (florent.barbault_at_univ-paris-diderot.fr)
Date: Mon May 25 2009 - 13:57:19 CDT

Hello,

I already had this message error from MMPBSA and the problem came from
the prmtop files. One way to verify easily the snapshot generation is
to create a pdb files of each of the three partners (com, rec and
lig).
ampbdb -p complex_without_wat.prmtop < com.crd.1 > test.pdb (you
should do the same with the receptor and the ligand)

Generally, if there is a problem a warning will appear. However, it
could be useful to have a look of the structure with your favorite
software...

Hope it will help you,
Regards
Florent Barbault

On Mon, 25 May 2009 17:58:41 +0200
  Rubben Torella <rubben.torella_at_gmail.com> wrote:
> Hi Amber users,
> I'm trying to calculate the binding free energy between a protein
>and a
> molecule.
> I have performed MD simulations, then I have picked the last
>snapshot from
> the MD simulation, I have stripped the water molecules and the
>counter-ions
> from it as explained in the tutorial, and I have built the parmtop
>of the
> ligand, receptor and complex, simply cutting from the pdb the
>coordinates of
> the atoms and then using xleap. Then I use the script in the example
>folder
> of mm_pbsa in order to create the snapshots of the complex, receptor
>and
> ligand.
> This script create the snapshot, I think correctly, but when I want
>to
> calculate the free energy of binding using the script of binding in
>the
> example folder, no output is created because of problem on the
>calculation
> of the energy...
> Here is my .log file errors:
> WARNING: Missing BOND for MM in 0 -> Taken from -1
> WARNING: Missing VDWNB for MM in 0 -> Taken from -1
> I have this warning for every snapshot.. and finally no calculation
>has been
> done.
> I don't know where is (are) my error (s)...
> Thank you in advance for every answer...
> Best regards
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor

NEW ADDRESS !!!

Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault_at_univ-paris-diderot.fr
-------------------------------------------------

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